Publications

Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags
Daniel, B. B. J., Steiger, Y., Sintsova, A., Field, C. M., Nguyen, B. D., Schubert, C., Cherrak, Y., Sunagawa, S., Hardt, W.-D., Vorholt, J. A. (2024).
https://doi.org/10.1038/s41564-024-01634-9
mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations
Sintsova, A., Ruscheweyh, H.-J., Field, C. M., Feer, L., Nguyen, B., Daniel, B., Hardt, W.-D., Vorholt, J. A., Sunagawa, S. (2024).
https://doi.org/10.1093/bioinformatics/btae078
From microbiome composition to functional engineering, one step at a time
Burz, S. D., Causevic, S., Dal Co, A., Dmitrijeva, M., Vonaesch, P., Vorholt, J., et al. (2023).
https://doi.org/10.1128/mmbr.00063-23
The microbiota conditions a gut milieu that selects for wild-type Salmonella Typhimurium virulence
Gül, E., Hardt, W.-D., et al. (2023).
https://doi.org/10.1371/journal.pbio.3002253
Differences in carbon metabolic capacity fuel co-existence and plasmid transfer between Salmonella strains in the mouse gut
Gül, E., Younes, A. A., Huuskonen, J., Diawara, C., Nguyen, B., Hardt, W.-D., et al. (2023).
https://doi.org/10.1016/j.chom.2023.05.029
Mouse models for bacterial enteropathogen infections: insights into the role of colonization resistance
Herzog, M., Cazzaniga, M., Peters, A., Shayya, N., Beldi, L., Hapfelmeier, S., Hardt, W.-D., et al. (2023).
https://doi.org/10.1080/19490976.2023.2172667
Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota
Hoces, D., Greter, G., Arnoldini, M., Stäubli, M., Moresi, C., Sintsova, A., Slack, E., et al. (2023).
https://doi.org/10.7554/eLife.81212
Chemotaxis and autoinducer-2 signalling mediate colonization and contribute to co-existence of Escherichia coli strains in the murine gut
Laganenka, L., Lee, J.-W., Malfertheiner, L., Dieterich, C. L., Fuchs, L., Piel, J., von Mering, C., Sourjik, V., Hardt, W.-D. (2023).
https://doi.org/10.1038/s41564-022-01286-7
Metabolic reconstitution of germ-free mice by a gnotobiotic microbiota varies over the circadian cycle
Hoces, D., Lan, J., Sun, W., Geiser, T., Stäubli, M., Barazzone, E., Arnoldini, M., Challa, T.D., Klug, M., Kellenberger, A., Nowok, S., Faccin, E., Macpherson, A.J., Stecher, B., Sunagawa, S., Zenobi, R., Hardt, W.-D., Wolfrum, C., Slack, E. (2022).
https://doi.org/10.1371/journal.pbio.3001743
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